The materials in the "Assigned Reading" column are directly
related to the topics covered in class. Readings under
"Additional Topics" are strictly optional and will not be covered
on the exams.
In some cases, the same material is covered in
more than one textbook. You have the choice of selecting the text
that presents a treatment of the material most to your liking. It
is your responsibility to make sure that you understand the
material covered in class and you may read as many or as few of
these texts needed to achieve that goal.





1.  Aug. 29 
PS0 out
Introduction to computational biology and genomics
part 1
, part 2
PS0, due September 5th in class solutions 
Review biology and algorithms background  
2.  Aug. 31 
Global pairwise sequence alignment
SEQUENCE ALIGNMENT NOTES Alignment example  distance scoring. 


3.  Sep. 5 
Global and semiglobal alignment
Alignment example  similarity scoring. PS0 DUE IN CLASS 


4.  Sep. 7 
Semiglobal and local pairwise alignment Local alignment examples PS1, due September 14th Alignment template solutions 
courtesy Dr. M. Singh, Princeton University 

5.  Sep. 12 
Local sequence alignment, local alignment examples Global multiple sequence alignment 711 Assignment 1, due September 28th , solutions Linear alignment template, Affine alignment template. 


6.  Sep. 14 
The progressive multiple alignment heuristic
PS1 due at 4pm. PS2 (due Friday, Sept 22nd). Alignment template Solutions 
Protein multiple sequence alignment , Do and Katoh, 2008.  
7.  Sep. 19 
Progressive multiple sequence alignment, continued. See Lecture 6 for slides. 

8.  Sep. 21 
Introduction to Markov chains
SEQUENCE EVOLUTION MODEL NOTES Includes Markov chains. PS2 due tomorrow, Sep 22. 


9.  Sep. 26 
Markov chains, continued PS3 (due Friday, Oct. 3). solutions 

10.  Sep. 28 
Markov models of sequence evolution,
JukesCantor model 711 Assignment 1 due 
Durbin, et al: 8.2, pp. 193  197 only (electronic reserves)  
11.  Oct. 3 
Markov models of nucleotide subtitution, continued.
PS3 due at 4pm 

12.  Oct. 5 
Inclass exam I This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study guide 

13.  Oct. 10 
Markov models of nucleotide subtitution, continued.


14.  Oct. 12 
Markov models of amino acid replacement
PS4 (due Friday, Oct. 20). solutions 

15.  Oct. 17 
AMINO ACID SCORING MATRICES 


16.  Oct. 19 
PS4 due tomorrow


17.  Oct. 24 
Blast heuristics BLAST LECTURE NOTES 


18.  Oct. 26  Blast statistics and information content 


19.  Oct. 31 
Blast statistics and information content. 

20.  Nov. 2 
Local multiple alignment, PSSM's, the Gibbs sampler slides PSSM example, with and without pseudocounts PS5 (due Friday, Nov. 10, 2pm). PAM250 matrix. solutions 


21.  Nov. 7 
PSSM, GIBBS SAMPLER LECTURE NOTES 711 Assignment 2, due Nov. 17th , solutions . 

22.  Nov. 9  Hidden Markov Models: Introduction 
Hidden Markov Models in Computational
Biology: Applications to Protein
Modeling, Krogh et al., JMB 235, pp 15011531,(1994). (electronic reserve). 

23.  Nov. 14 
Inclass exam II This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study guide 

24.  Nov. 16 
HIDDEN MARKOV MODELS LECTURE NOTES
HMMs cont'd. Recognition: the Forward algorithm Forward example 

25.  Nov. 21 
No class.
711 Assignment 3, due WEDNESDAY Nov. 29th, 4pm; solutions . 

Nov. 23 
Thanksgiving Holiday: No class 

26.  Nov. 28 
Hidden Markov Models: Decoding Viterbi example PS6, solutions (due Thurs., Dec 7th). 

27.  Nov. 30 
HMMs:
Modeling
711 Assignment 4, due Friday, Dec 8th, 4pm. Solutions  
28.  Dec. 5 
Profile HMM's.

 
29.  Dec. 7 
Profile HMMs,
Hidden Markov Models for global multiple alignment Optional PS7, due Wednesday, 13th at 1pm if you are submitting PS 7 for credit. Solutions 


Final exam  Dec 17, 1pm 4pm
GHC 4215 
Final exam
This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. 
Study guide The exam covers the entire semester, but with a strong emphasis on the last third of the course. 
The time and date of the final exam are determined by the
registrar's office and are beyond my control. You must take the
final exam at the time scheduled.
Until the date of
the final is determined, you should not make plans to leave for
winter vacation before the end of the exam period.
